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E-GEOD-59479 - Gene expression analysis to identify long noncoding RNAs deregulated in Myc-driven B cell lymphoma

Status
Released on 1 February 2015, last updated on 8 February 2015
Organism
Homo sapiens
Samples (22)
Array (1)
Protocols (5)
Description
Myc is a well known transcription factor with important roles in cell cycle, apoptosis and cellular transformation. Long non-coding (lnc)RNAs have recently emerged as a important class of regulatory RNAs. Here, we show that lncRNAs are an extensive component of the Myc-regulated transcriptional program. Using the P493-6 inducible Myc model we demonstrate that both Myc-induced mRNAs and lncRNAs were significant enriched for Myc binding sites. In contrast to Myc-repressed mRNAs, Myc-repressed lncRNAs were significantly enriched for Myc binding sites. Subcellular localization analysis revealed that Myc-repressed lncRNAs and mRNAs are enriched in the nucleus while Myc-induced lncRNAs and mRNAs are enriched both in the cytoplasm and nucleus. Parallel analysis of differentially expressed lncRNAs and mRNAs identified 105 lncRNA-mRNA pairs that were in close vicinity, indicative for regulation in cis. To support the potential relevance of the Myc-regulated lncRNAs in cellular transformation, we analyzed their expression in primary Myc-high and Myc-low B-cell lymphomas. In total, 54% of the lncRNAs differentially expressed between the lymphoma subsets were identified as Myc-regulated in P493-6 cells. This study is the first to show that lncRNAs are an important factor within the Myc-regulated transcriptional program and indicates a marked difference between Myc-repressed lncRNAs and mRNAs. Expression of all known mRNAs and >10 000 lncRNAs was assessed in primary lymphoma tissue with high c-myc levels (Burkitt lymphoma; BL) and low c-myc levels (chronic lymphocytic leukemia; CLL)
Experiment type
transcription profiling by array 
Contacts
Melanie Winkle <melanie.winkle@gmail.com>, Anke van den Berg, Arjan Diepstra, Debora de Jong, Gertrud Kortman, Jantine Sietzema, Joost Kluiver, Klaas Kok, Lydia Visser, Martijn Terpstra, Masoumeh Tayari
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-59479.idf.txt
Sample and data relationshipE-GEOD-59479.sdrf.txt
Raw data (1)E-GEOD-59479.raw.1.zip
Processed data (1)E-GEOD-59479.processed.1.zip
Array designA-GEOD-18959.adf.txt
Links